The Euscaphis japonica genome and the evolution of malvids

Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, an early-diverging species within malvids. Genome-based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the c event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit-hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission.DATA AVAILABILITY STATEMENT : All sequences described in this manuscript have been submitted to the National Genomics Data Center (NGDC). The raw whole-genome data of E. japonica have been deposited in BioProject/GSA (https://bigd.big.ac.cn/gsa.) under the accession codes PRJCA005268/CRA004271, and the assembly and annotation data have been deposited at BioProject/GWH (https://bigd.big.ac.cn/gwh) under the accession codes PRJCA005268/GWHBCHS00000000. The raw transcriptomes data of E. japonica have been deposited in BioProject/GSA (https://bigd.big.ac.cn/gsa.) under the accession codes PRJCA005298/CRA004272.SUPPLEMENTARY MATERIAL 1: Supplementary Note 1. Chromosome number assessment. Supplementary Note 2. Whole-genome duplication identification and dating. Supplementary Note 3. Observation of E. japonica seed dispersal. Supplementary Note 4. Determination of pentacyclic triterpene substances. Figure S1. Cytogenetic analysis of E. japonica. Figure S2. Genome size and heterozygosity of E. japonica estimation using 17 k-mer distribution. Figure S3. Interchromosomal of Hi-C chromosome contact map of E. japonica genome. Figure S4. Gene structure prediction results of E. japonica and other species. Figure S5. Venn diagram shows gene families of malvids. Figure S6. Phylogenetic tree constructed by chloroplast genomes from 17 species. Figure S7. Concatenated- and ASTRAL-based phylogenetic trees. Figure S8. Ks distribution in E. japonica. Figure S9. Distributions of synonymous substitutions per synonymous site (Ks) of one-to-one orthologs identified between E. japonica and P. trichocarpa and V. vinifera. Figure S10. Population structure plot. Figure S11. Fixation index (FST) heat map among E. japonica populations. Figure S12. Phylogenetic analysis of MADS-box genes from O. sativa, A. thaliana, E. japonica, and T. cacao. Figure S13. Observation the fruit development. Figure S14. Animal seed dispersal. Figure S15. Anthocyanin biosynthesis in E. japonica fruits. Figure S16. Carotenoid accumulation and the chlorophyll degradation in E. japonica fruits. Figure S17. Expression profile of fruit dehiscence-related genes. Figure S18. Phylogenetic tree of DELLA genes obtained from six malvids species. Figure S19. Phylogenetic tree of CAD genes obtained from seven malvids species. Figure S20. Expression pattern of fruit abscission-related genes. Figure S21. Structure of pentacyclic triterpene compounds separated from Euscaphis. Figure S22. Phylogenetic tree of HMGR gene in plants. Figure S23. Phylogenetic tree of P450s gene family obtained from A. thaliana and E. japonica.SUPPLEMENTARY MATERIAL 2: Table S1. Assembled statistics of E. japonica genome. Table S2. Evaluation of E. japonica genome assembly. Table S3. Chromosome length of E. japonica. Table S4. Prediction of gene structures of the E. japonica genome. Table S5. Statistics on the function annotation of the E. japonica genome. Table S6. Non-coding RNA annotation results of E. japonica genome. Table S7. BUSCO assessment of the E. japonica annotated genome. Table S8. Statistic of repeat sequence in E. japonica genome. Table S9. Gene-clustering statistics for 17 species. Table S10. KEGG enrichment result of unique genes families of E. japonica. Table S11. Gene Ontology (GO) and KEGG enrichment result of significant shared by malvids species gene families. Table S12. Gene Ontology (GO) and KEGG enrichment result of significant expansion of E. japonica gene families. Table S13. Gene Ontology (GO) enrichment result of significant contraction of E. japonica gene families. Table S14. Statistical sampling population information. Table S15. Statistics population resequencing information. Table S16. Statistical nucleotide polymorphisms in the populations. Table S17. Candidate positive selection genes (PSGs) in the evergreen population. Table S18. Candidate positive selection genes (PSGs) in the deciduous population. Table S19. Gene Ontology (GO) enrichment result of significant PSGs in the evergreen population. Table S20. List of MADS-box genes identified in E. japonica. Table S21. Genes involved in anthocyanin biosynthesis, carotenoid biosynthesis, and chlorophyll degradation. Table S22. Identification fruit dehiscence-related genes in E. japonica. Table S23. Genes related to lignin synthesis that are highly expressed during pericarp dehiscence. Table S24. Gene expression levels (FPKMs) of fruit abscission-related genes in pericarp. Table S25. Triterpene compounds separated from Euscaphis. Table S26. Number of putative pentacyclic triterpene-related genes in the malvids species. Table S27. Identified pentacyclic triterpene synthesis-related genes in E. japonica genome. Table S28. Statistical simple sequence repeat.Fund for Excellent Doctoral Dissertation of Fujian Agriculture and Forestry University, China; Fujian Provincial Department of Science E. japonica Evolution and Selection of Ornamental Medicinal Resources, China; the Project of Forestry Peak Discipline at Fujian Agriculture and Forestry University, China; the Collection, Development and Utilization of Eascaphis konlshli Germplasm Resources; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program and from Ghent University.https://onlinelibrary.wiley.com/journal/1365313xam2022BiochemistryGeneticsMicrobiology and Plant Patholog

The Synthesis of Mesoporous TS-1 and Its Performance for Oxidation of Diphenyl Sulfide and Dibenzyl Sulfide

TS-1 zeolite has outstanding performance in the catalytic reactions with hydrogen peroxide as catalytic promoter. However, the narrow pore size (< 1.0 nm) of traditional TS-1 makes it difficult for bulky organic compounds to contact with the active sites in the pores, which seriously limits application of TS-1. Recently, the introduction of mesoporous structure into microporous TS-1 becomes a hot research topic. Meanwhile, the huge synthesis cost of TS-1 is another main reason hindering its industrial application. In this paper, mesoporous TS-1 was successfully synthesized using sodium silicate as silicon source and titanium trichloride as titanium source under the template conditions of tetrapropylammonium hydroxide (TPAOH) and cationic polymer. The mesoporous TS-1 was characterized by X-ray diffraction (XRD), N2 adsorption, scanning electric microscopy (SEM), transmitting electric microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR) and UV-Vis Spectrum spectra (UV-Vis). Results show that the synthesized TS-1 zeolites have good crystallinity and tetra-coordinated framework Ti atoms, and there are abundant mesoporous structures in the zeolite crystals. The results of oxidation experiments show that conversion of diphenyl sulfide and dibenzyl sulfide with mesoporous TS-1 are 97.3 % and 85.3 % respectively, while that conversion with microporous TS-1 are 75.7 % and 63.5 respectively

Active Compounds Derived from Fuzheng Huayu Formula Protect Hepatic Parenchymal Cells from Apoptosis Based on Network Pharmacology and Transcriptomic Analysis

Fuzheng huayu formula (FZHY), an antifibrotic traditional Chinese medicine, is frequently used for the treatment of liver fibrosis. In this study, network analysis, transcriptomic analysis, assays of cell apoptosis, viability and protein expression were used for investigating the effects and mechanisms of compounds derived from FZHY on hepatic parenchymal cell (HPC) protection and hepatic stellate cell activation. Network pharmacology analysis found that 6 major compounds and 39 potential targets were important network nodes. Our analysis predicted that the active compounds of FZHY, including hederagenin, luteolin and tanshinone IIA inhibited cell apoptosis (p &lt; 0.05), increased PI3K expression and reduced cleaved caspase 3 expression and the Bax/Bcl-w ratio (p &lt; 0.05) in L02 cells that had apoptosis induced by TNF-&alpha;. Few significant changes caused by FZHY, hederagenin, luteolin and tanshinone IIA were observed in hepatic stellate Lx2 cells upon TGF-&beta;1 induction. These data suggest that FZHY is active against liver fibrosis, protects hepatic parenchymal cells from apoptosis, and recovers liver function, possibly through the effects of its active compounds hederagenin, luteolin and tanshinone IIA and is involved in the inhibition of apoptosis in HPCs, possibly through regulating the PI3K, ERK, cleaved caspase 3 and Bax/Bcl-w levels

Effects of Barranca yajiagengensis Powder in the Diet of Trachinotus ovatus on the Growth Performance, Antioxidant Capacity, Immunity and Morphology of the Liver and Intestine

Barranca yajiagengensis, a novel filamentous microalga, can accumulate lutein under high-light and low-nitrogen conditions. It is well known that lutein has antioxidant, anti-inflammatory and immune-modulating properties. The purpose of this study is to evaluate the effects of including lutein-rich B. yajiagengensis powder in the diet of Trachinotus ovatus on the growth performance, antioxidant capacity, immunity, liver, and intestinal morphology. For this aim, three experimental diets containing 0% (BY0), 1% (BY1), and 5% (BY5) B. yajiagengensis powder were formulated for six-week feeding trials. The results indicated that growth performance, feed utilization, and intestinal morphology were not affected by different diet treatments. Fish fed with the BY5 diet promoted antioxidant ability by activating the Nrf2-ARE signal pathway and enhancing antioxidant enzymes activities. Furthermore, the BY5 diet improved non-specific immunity and antibacterial ability by activating lysozymes and the complement system and increasing the nitric oxide (NO) content and total nitric oxide synthase activity. Dietary B. yajiagengensis supplementation improved the liver morphology and exerted hepatoprotective effects. Therefore, as a natural source of lutein, B. yajiagengensis has the potential as a safe and non-toxic immunostimulant for T. ovatus. A diet supplemented with 5% B. yajiagengensis is recommended to improve the growth, antioxidant capacity, immune response, and liver health of T. ovatus

Altered adolescents obesity metabolism is associated with hypertension: a UPLC-MS-based untargeted metabolomics study

ObjectiveThis study aimed to explore the relationship between the plasma metabolites of adolescent obesity and hypertension and whether metabolite alterations had a mediating effort between adolescent obesity and hypertension.MethodsWe applied untargeted ultra-performance liquid chromatography–mass spectrometry (UPLC-MS) to detect the plasma metabolomic profiles of 105 adolescents. All participants were selected randomly based on a previous cross-sectional study. An orthogonal partial least squares- discriminant analysis (OPLS-DA), followed by univariate statistics and enrichment analysis, was used to identify differential metabolites. Using logistic regression for variable selection, an obesity-related metabolite score (OMS, OMS=∑k=1nβnmetabolite n) was constructed from the metabolites identified, and hypertension risk was estimated.ResultsIn our study, based on P&lt; 0.05, variable importance in projection (VIP) &gt; 1.0, and impact value &gt; 0.1, we identified a total of 12 differential metabolites. Significantly altered metabolic pathways were the sphingolipid metabolism, purine metabolism, pyrimidine metabolism, phospholipid metabolism, steroid hormone biosynthesis, tryptophan, tyrosine, and phenylalanine biosynthesis. The logistic regression selection resulted in a four-metabolite score (thymidine, sphingomyelin (SM) d40:1, 4-hydroxyestradiol, and L-lysinamide), which was positively associated with hypertension risk (odds ratio: 7.79; 95% confidence interval: 2.13, 28.47; for the quintile 4 compared with quartile 1 of OMS) after multivariable adjustment.ConclusionsThe OMS constructed from four differential metabolites was used to predict the risk of hypertension in adolescents. These findings could provide sensitive biomarkers for the early recognition of hypertension in adolescents with obesity

Network Pharmacology-Based Study on the Mechanism of Bushen-Jianpi Decoction in Liver Cancer Treatment

To investigate the mechanism of a Bushen-Jianpi decoction (BSJPD) in liver cancer (LC) treatment, we analyzed clinical therapy data, conducted network pharmacology analysis, and performed pharmacological experimental verification in vitro and in vivo. The univariate analysis of clinical therapy showed that the BSJPD was protective factor (p < 0.05). The network pharmacology analysis showed that 9 compounds were important nodes of BSJPD-LC therapy network. In experimental verification, the rate of apoptosis increased in the liver tumors of mice treated with the BSJPD (p < 0.05); drug serum with 20 % BSJPD inhibited cell viability (p < 0.05) and reduced the expression of PI3K, the Bcl-xL/BAD ratio, and the levels of p53 and p-Akt in HepG2 cells. Moreover, licochalcone A, alisol B, and hederagenin inhibited cell viability (p < 0.05), induced cell apoptosis (p < 0.01), reduced p-Akt levels, and increased cleaved-CASP3 (p < 0.05) and p53 expression levels in HepG2 cells. These data suggest that the BSJPD prolongs the survival of LC patients and induces apoptosis and that it may be associated with the regulation of PI3K, Akt, p53, CASP3, and Bcl-xL/BAD expression